Eduardo Davila

Rare melanoma subtypes, including acral, mucosal, and uveal melanomas, exhibit limited responses to immune checkpoint inhibitors (ICI), yet the molecular mechanisms of immune resistance remain poorly defined. This study aimed to characterize transcriptional programs associated with immune evasion across melanoma subtypes and identify strategies to restore immune gene expression in rare melanomas. We performed transcriptomic profiling of xenografts derived from patients with melanoma and publicly available tumor datasets to compare intratumoral gene expression across cutaneous and rare melanoma subtypes. Cross-subtype analysis revealed convergent downregulation of innate immune pathogen sensing (IIPS) and type I interferon signaling pathways in rare melanomas compared with cutaneous tumors. Lower IIPS expression correlated with nonresponse to PD-1 blockade, which was associated with reduced CD8+ and memory CD4+ T-cell infiltration and enrichment of M2 macrophages inferred by CIBERSORT. Immunomodulatory compounds were screened in vitro to identify IIPS-inducing drugs, and decitabine was further evaluated in mucosal and uveal melanoma xenograft models. Decitabine treatment robustly induced IIPS and antigen presentation genes in rare melanoma cell lines and xenografts, with RNA sequencing confirming IIPS reexpression as the dominant transcriptional consequence. Silencing of IIPS genes represents a recurrent immune evasion mechanism in rare melanomas. Decitabine reverses this silencing, restoring innate and adaptive immune gene expression, and may serve as a therapeutic priming strategy to enhance ICI responsiveness in patients with rare melanoma subtypes.

Figure S1. Study design and treatment schedule

Generalizability to sarcoma population

Complete clinical and genetic details of patients

Figure S2. Representative cross-sectional imaging for selected responding patients.

Figure S3. Post-hoc analysis comparing stage 1 and stage 2 clinical outcomes.

Serum cytokines from Luminex analysis not included in the main figures and cytokine levels in tumor interstitial fluid

Flow gating strategy and TIL phenotypes not included in the main figures

Appending CD3ζ:MyD88 to the TCR α-chain and the α- and β chain concurrently prevents the TCR from being expressed and appending CD3ζ:MyD88 to the TCR β chain increases IFNg production following TCR stimulation